Jeff Evans
I have come from an era right back in the analog tape multi track days where I was producing a lot of synthesiser music and printing audio from midi parts etc and the tape playback was never as good as the synth playing in real life yet somehow it was not such a big deal. I think today I can honestly say we have got some amazing quality now in this area and really transferring  either external synth parts to audio or rendering internal synths has really never been better.
 
What Craig is saying is true in terms of synths having lots of internal modulations going on even if they are subtle so every time you render you are going to get very slight variations. The only time you may get close to prefect nulls etc is with sounds that are very static and have no movement whatsoever programmed into them and they are usually very few.  We tend to not like those types of sounds.  But in some situations they can actually work better.
 
The level variations may be coming from the fact that when you try to null things out because LFO's are in varying parts of their cycles and are not synchronised anywhere, that is where there may be some slight cancellations going on.
 
I do agree though that some synths e.g. Omnisphere (there was a bug for a while with fast bounces etc) may prefer real time renders because fast bounces can play havoc with some the more very deep and complex instruments with huge effects processing going on etc...
 
 

 
I think I may have misled with my previous statement - the level variations aren't happening when nulling things out, they're noticeable when comparing the original with the exported track separately. I will for instance play the first measure of the original part, note the peak level, then do the same with the exported version. I totally get what you're saying about LFO's, but I have all modulation turned off in the synth for this part. So with the analog modeling I'd expect to hear maybe some quiet information when nulling them, what I'm hearing instead sounds like everything from the mids upwards as if I've applied a HPF at around 400-500Hz. 
 

Did you sum a stereo patch to mono perhaps?

Does this only occur using Elements or with other synths as well? With all patches or only some? What happens if you program a patch yourself using a single oscillator, wide open low pass filter, envelopes with attack, decay and release at zero and no modulation sources in use?

I have a feeling I might have an explanation for why Elements may be doing what it is but it's long and answers to those questions might show I'm heading off down a blind alley so I'll not post it yet.

How about trying to record the soft synth directly to an audio track?  Splat can do that now ...

Sanderxpander
Did you sum a stereo patch to mono perhaps?

Nope export was set to follow source. Both tracks are mono, and the input of the original track is a mono output from Element.  

tlw
Does this only occur using Elements or with other synths as well? With all patches or only some? What happens if you program a patch yourself using a single oscillator, wide open low pass filter, envelopes with attack, decay and release at zero and no modulation sources in use?

I have a feeling I might have an explanation for why Elements may be doing what it is but it's long and answers to those questions might show I'm heading off down a blind alley so I'll not post it yet.

I'm going to try out some things like that later if I have time.

abacab
How about trying to record the soft synth directly to an audio track?  Splat can do that now ...

Yeah I do that a lot too, the only thing is I don't trust that either because sometimes I find the timing of the original and the source are a little off. I had this a while ago when I tried to record a kick drum from Geist directly onto a track. What I ended up with was a few ticks away from the original such that when played together, there was a little cancelling. 

sharke

Sanderxpander
Did you sum a stereo patch to mono perhaps?

Nope export was set to follow source. Both tracks are mono, and the input of the original track is a mono output from Element.  

Sorry for being really vague here but I remember reading about some bugfix where "follow source" didn't work correctly, maybe the 2016.12 or the 2017.01 update.